AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene80639


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene80639.t1 MTR_5g081705 100.000 112 0 0 1 112 26 137 1.99e-79 229
MS.gene80639.t1 MTR_0699s0020 94.643 112 6 0 1 112 1 112 3.79e-77 223
MS.gene80639.t1 MTR_0699s0010 93.750 112 7 0 1 112 1 112 1.49e-76 221
MS.gene80639.t1 MTR_5g081705 100.000 99 0 0 1 99 26 124 3.59e-69 203
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene80639.t1 AT1G74270 88.393 112 13 0 1 112 1 112 9.66e-73 212
MS.gene80639.t1 AT1G07070 87.500 112 14 0 1 112 1 112 9.87e-73 212
MS.gene80639.t1 AT3G55750 89.189 111 12 0 2 112 1 111 6.67e-72 209
MS.gene80639.t1 AT1G41880 88.288 111 13 0 2 112 1 111 9.58e-72 209
MS.gene80639.t1 AT1G41880 88.288 111 13 0 2 112 1 111 9.58e-72 209

Find 44 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAAGAATTACCATTGATTT+TGG 0.162742 5.4:-64410309 None:intergenic
GCACCAATCAAAATGGTTAA+AGG 0.315193 5.4:+64409302 None:intergenic
TATGTCAGGGGCACAGTTCT+TGG 0.316095 5.4:+64409449 MS.gene80639:CDS
GAAGCCACTATCGCTGCATT+TGG 0.347853 5.4:+64410220 MS.gene80639:CDS
ATTTGTTTGTGCAGGGAGCC+AGG 0.348132 5.4:+64410402 MS.gene80639:intron
AAGCCACTATCGCTGCATTT+GGG 0.372191 5.4:+64410221 MS.gene80639:CDS
ATGTATCCAAGCAATATATA+AGG 0.407008 5.4:+64410437 MS.gene80639:CDS
ATCTGAACAAGAGAGGTGTT+TGG 0.408357 5.4:-64410111 None:intergenic
AAATTACCTTATATATTGCT+TGG 0.412163 5.4:-64410443 None:intergenic
GAGGAGGTTGCATGGTATGC+TGG 0.417733 5.4:+64410153 MS.gene80639:CDS
ACCTCTCTTGTTCAGATTGA+GGG 0.421870 5.4:+64410117 MS.gene80639:CDS
TCTGAACAAGAGAGGTGTTT+GGG 0.426207 5.4:-64410110 None:intergenic
CTATCGCTGCATTTGGGGTA+AGG 0.428656 5.4:+64410227 MS.gene80639:CDS
CACCTCTCTTGTTCAGATTG+AGG 0.448350 5.4:+64410116 MS.gene80639:CDS
TACCCCAAATGCAGCGATAG+TGG 0.457668 5.4:-64410224 None:intergenic
GACGTCAAGGAGAACGCATC+AGG 0.461646 5.4:+64409324 MS.gene80639:CDS
GTTTGGGTATTGATTTACCT+TGG 0.466066 5.4:-64410094 None:intergenic
ATGGTATGCTGGGAAGAAAT+TGG 0.469927 5.4:+64410164 MS.gene80639:CDS
GCTTCCATCCTTCTTCACCT+TGG 0.472167 5.4:-64410202 None:intergenic
GCATTTGGGGTAAGGTTACC+AGG 0.512393 5.4:+64410235 MS.gene80639:CDS
ATACCATGCAACCTCCTCCT+TGG 0.519241 5.4:-64410148 None:intergenic
GCCACTGTTACCATGAGGCC+TGG 0.523824 5.4:-64410253 None:intergenic
AGGAGGTTGCATGGTATGCT+GGG 0.527652 5.4:+64410154 MS.gene80639:CDS
TTTGTTTGTGCAGGGAGCCA+GGG 0.534698 5.4:+64410403 MS.gene80639:intron
TTTAATCAGGCTTTATGTCA+GGG 0.536616 5.4:+64409436 MS.gene80639:intron
TTACAAGGCCAAGGTGAAGA+AGG 0.537680 5.4:+64410194 MS.gene80639:CDS
TAACCTACCACCAAAATCAA+TGG 0.539094 5.4:+64410299 MS.gene80639:CDS
GGCATACATTTACAAGGCCA+AGG 0.547418 5.4:+64410185 MS.gene80639:CDS
GAAATTGGCATACATTTACA+AGG 0.562532 5.4:+64410179 MS.gene80639:CDS
GTGATGTTGTTATAGGTCCA+AGG 0.578714 5.4:+64410077 MS.gene80639:intron
ATACATAAATACTCTAACCC+TGG 0.583670 5.4:-64410420 None:intergenic
GGTAAGGTTACCAGGCCTCA+TGG 0.585246 5.4:+64410243 MS.gene80639:CDS
AAGGCCAAGGTGAAGAAGGA+TGG 0.591334 5.4:+64410198 MS.gene80639:CDS
ACACCAAGGAGGAGGTTGCA+TGG 0.606757 5.4:+64410145 MS.gene80639:CDS
TTAATCAGGCTTTATGTCAG+GGG 0.608287 5.4:+64409437 MS.gene80639:intron
CCTCTCTTGTTCAGATTGAG+GGG 0.617526 5.4:+64410118 MS.gene80639:CDS
AAAATGGTTAAAGGACGTCA+AGG 0.620787 5.4:+64409311 None:intergenic
GGTTAGACTTGAACTTTGCG+CGG 0.621246 5.4:-64410281 None:intergenic
AGCCACTATCGCTGCATTTG+GGG 0.627011 5.4:+64410222 MS.gene80639:CDS
GCACAGTTCTTGGATACAAG+AGG 0.637980 5.4:+64409459 MS.gene80639:CDS
CCCCTCAATCTGAACAAGAG+AGG 0.640107 5.4:-64410118 None:intergenic
CTCTCTTGTTCAGATTGAGG+GGG 0.642105 5.4:+64410119 MS.gene80639:CDS
ACCAGGCCTCATGGTAACAG+TGG 0.661908 5.4:+64410252 MS.gene80639:CDS
ACAATGCCACTGTTACCATG+AGG 0.746625 5.4:-64410258 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATGAAAATAACAACATT+AGG - chr5.4:64409411-64409430 None:intergenic 15.0%
!! AAGCTAATTAAATCTAATTT+GGG + chr5.4:64409559-64409578 MS.gene80639:intron 15.0%
!! AATAAAATCAAAAGAGTTAA+AGG - chr5.4:64409377-64409396 None:intergenic 15.0%
!! TAAGCTAATTAAATCTAATT+TGG + chr5.4:64409558-64409577 MS.gene80639:intron 15.0%
!!! AATATATGATTTTTTTAGCT+GGG + chr5.4:64409602-64409621 MS.gene80639:intron 15.0%
!!! AATTCTTTAAGACATTTAAA+TGG + chr5.4:64410323-64410342 MS.gene80639:intron 15.0%
!!! TAATATATGATTTTTTTAGC+TGG + chr5.4:64409601-64409620 MS.gene80639:intron 15.0%
!! AAATGATTACTGTAAGATTT+GGG + chr5.4:64409897-64409916 MS.gene80639:intron 20.0%
!! CGGAAGAAAAATTATATATT+TGG - chr5.4:64409973-64409992 None:intergenic 20.0%
!! TAAATGATTACTGTAAGATT+TGG + chr5.4:64409896-64409915 MS.gene80639:intron 20.0%
!!! TAAAGAATTACCATTGATTT+TGG - chr5.4:64410312-64410331 None:intergenic 20.0%
!!! TTCATTTTGTGTTTTTAATC+AGG + chr5.4:64409423-64409442 MS.gene80639:intron 20.0%
!!! TTTGGGTATTATTTTTTGTA+TGG + chr5.4:64409914-64409933 MS.gene80639:intron 20.0%
! ACAAACACAAATTAAAAGCT+GGG - chr5.4:64409728-64409747 None:intergenic 25.0%
! ATCAAAATCAAGAACTACTA+GGG - chr5.4:64410016-64410035 None:intergenic 25.0%
! GATTATTTGTGCTAAGAAAT+TGG + chr5.4:64410055-64410074 MS.gene80639:intron 25.0%
!! ATATTTTATCGAGGATACAT+TGG - chr5.4:64409806-64409825 None:intergenic 25.0%
!! TATTTTATCGAGGATACATT+GGG - chr5.4:64409805-64409824 None:intergenic 25.0%
!! TTGGGTATTATATTTTATCG+AGG - chr5.4:64409815-64409834 None:intergenic 25.0%
!!! ATGTTTAATGTTGTTTTAGC+TGG + chr5.4:64409643-64409662 MS.gene80639:intron 25.0%
!!! TTTTTCAGTTTTTGCTGTAT+TGG + chr5.4:64409506-64409525 MS.gene80639:intron 25.0%
!!! TTTTTTTAGCTGGGTTTTAT+TGG + chr5.4:64409611-64409630 MS.gene80639:intron 25.0%
ATACATAAATACTCTAACCC+TGG - chr5.4:64410423-64410442 None:intergenic 30.0%
CACAAACACAAATTAAAAGC+TGG - chr5.4:64409729-64409748 None:intergenic 30.0%
CATCAAAATCAAGAACTACT+AGG - chr5.4:64410017-64410036 None:intergenic 30.0%
GAAATTGGCATACATTTACA+AGG + chr5.4:64410179-64410198 MS.gene80639:CDS 30.0%
TTAAGAACCAAGACTCAATT+TGG + chr5.4:64409759-64409778 MS.gene80639:intron 30.0%
TTCAGAAACCATAAAACAGT+TGG - chr5.4:64410369-64410388 None:intergenic 30.0%
! CATTTTCACCAACTGTTTTA+TGG + chr5.4:64410358-64410377 MS.gene80639:intron 30.0%
! TTTAATCAGGCTTTATGTCA+GGG + chr5.4:64409436-64409455 MS.gene80639:intron 30.0%
! TTTATGGTTTCTGAAAGCTT+TGG + chr5.4:64410374-64410393 MS.gene80639:intron 30.0%
!! CTTGATTTTGATGTTGATCT+GGG + chr5.4:64410024-64410043 MS.gene80639:intron 30.0%
!! GAAATTGGTGATGTTGTTAT+AGG + chr5.4:64410070-64410089 MS.gene80639:intron 30.0%
!! TCTTGATTTTGATGTTGATC+TGG + chr5.4:64410023-64410042 MS.gene80639:intron 30.0%
!! TTTTAATCAGGCTTTATGTC+AGG + chr5.4:64409435-64409454 MS.gene80639:intron 30.0%
!!! AGAATTACCATTGATTTTGG+TGG - chr5.4:64410309-64410328 None:intergenic 30.0%
AGTTAAAGGATACAGATCGA+AGG - chr5.4:64409363-64409382 None:intergenic 35.0%
GTTAAAGGATACAGATCGAA+GGG - chr5.4:64409362-64409381 None:intergenic 35.0%
TAACCTACCACCAAAATCAA+TGG + chr5.4:64410299-64410318 MS.gene80639:CDS 35.0%
TGAAGACACATTATGTACGA+CGG - chr5.4:64409993-64410012 None:intergenic 35.0%
TTGGTCCTTCACAATATTTG+CGG + chr5.4:64409778-64409797 MS.gene80639:intron 35.0%
! TTAATCAGGCTTTATGTCAG+GGG + chr5.4:64409437-64409456 MS.gene80639:intron 35.0%
!! GTTTGGGTATTGATTTACCT+TGG - chr5.4:64410097-64410116 None:intergenic 35.0%
!!! TTACCATTGATTTTGGTGGT+AGG - chr5.4:64410305-64410324 None:intergenic 35.0%
ACCTCTCTTGTTCAGATTGA+GGG + chr5.4:64410117-64410136 MS.gene80639:CDS 40.0%
ATGGTATGCTGGGAAGAAAT+TGG + chr5.4:64410164-64410183 MS.gene80639:CDS 40.0%
CCTAGACTCATTATCACAAG+CGG - chr5.4:64409874-64409893 None:intergenic 40.0%
GTGATGTTGTTATAGGTCCA+AGG + chr5.4:64410077-64410096 MS.gene80639:intron 40.0%
TGAAGGACCAAATTGAGTCT+TGG - chr5.4:64409769-64409788 None:intergenic 40.0%
TGGTCCTTCACAATATTTGC+GGG + chr5.4:64409779-64409798 MS.gene80639:intron 40.0%
!! ATCTGAACAAGAGAGGTGTT+TGG - chr5.4:64410114-64410133 None:intergenic 40.0%
!! GATAATGCTGGGACTAGTTT+GGG - chr5.4:64409833-64409852 None:intergenic 40.0%
!! GGTGTTGATTTGTTTGTGCA+GGG + chr5.4:64410395-64410414 MS.gene80639:intron 40.0%
!! TCTGAACAAGAGAGGTGTTT+GGG - chr5.4:64410113-64410132 None:intergenic 40.0%
!! TGATAATGCTGGGACTAGTT+TGG - chr5.4:64409834-64409853 None:intergenic 40.0%
!! TGGTGTTGATTTGTTTGTGC+AGG + chr5.4:64410394-64410413 MS.gene80639:intron 40.0%
AAGCCACTATCGCTGCATTT+GGG + chr5.4:64410221-64410240 MS.gene80639:CDS 45.0%
ACAATGCCACTGTTACCATG+AGG - chr5.4:64410261-64410280 None:intergenic 45.0%
CACCTCTCTTGTTCAGATTG+AGG + chr5.4:64410116-64410135 MS.gene80639:CDS 45.0%
CCTCTCTTGTTCAGATTGAG+GGG + chr5.4:64410118-64410137 MS.gene80639:CDS 45.0%
CTCTCTTGTTCAGATTGAGG+GGG + chr5.4:64410119-64410138 MS.gene80639:CDS 45.0%
GCACAGTTCTTGGATACAAG+AGG + chr5.4:64409459-64409478 MS.gene80639:CDS 45.0%
GGCATACATTTACAAGGCCA+AGG + chr5.4:64410185-64410204 MS.gene80639:CDS 45.0%
GGTTAGACTTGAACTTTGCG+CGG - chr5.4:64410284-64410303 None:intergenic 45.0%
TCCCAGCATTATCACAGTAC+AGG + chr5.4:64409840-64409859 MS.gene80639:intron 45.0%
TTACAAGGCCAAGGTGAAGA+AGG + chr5.4:64410194-64410213 MS.gene80639:CDS 45.0%
TTGATGTTGATCTGGGTTGC+TGG + chr5.4:64410031-64410050 MS.gene80639:intron 45.0%
! CCGCTTGTGATAATGAGTCT+AGG + chr5.4:64409871-64409890 MS.gene80639:intron 45.0%
! GCCTGTACTGTGATAATGCT+GGG - chr5.4:64409844-64409863 None:intergenic 45.0%
! TGCCTGTACTGTGATAATGC+TGG - chr5.4:64409845-64409864 None:intergenic 45.0%
AAGGCCAAGGTGAAGAAGGA+TGG + chr5.4:64410198-64410217 MS.gene80639:CDS 50.0%
AGCCACTATCGCTGCATTTG+GGG + chr5.4:64410222-64410241 MS.gene80639:CDS 50.0%
AGGAGGTTGCATGGTATGCT+GGG + chr5.4:64410154-64410173 MS.gene80639:CDS 50.0%
ATACCATGCAACCTCCTCCT+TGG - chr5.4:64410151-64410170 None:intergenic 50.0%
ATTTGTTTGTGCAGGGAGCC+AGG + chr5.4:64410402-64410421 MS.gene80639:intron 50.0%
CCCCTCAATCTGAACAAGAG+AGG - chr5.4:64410121-64410140 None:intergenic 50.0%
GAAGCCACTATCGCTGCATT+TGG + chr5.4:64410220-64410239 MS.gene80639:CDS 50.0%
GATTGAGGGGGTAAACACCA+AGG + chr5.4:64410131-64410150 MS.gene80639:CDS 50.0%
GCTTCCATCCTTCTTCACCT+TGG - chr5.4:64410205-64410224 None:intergenic 50.0%
TACCCCAAATGCAGCGATAG+TGG - chr5.4:64410227-64410246 None:intergenic 50.0%
TGGGCCCGCAAATATTGTGA+AGG - chr5.4:64409786-64409805 None:intergenic 50.0%
TTTGTTTGTGCAGGGAGCCA+GGG + chr5.4:64410403-64410422 MS.gene80639:intron 50.0%
! CTATCGCTGCATTTGGGGTA+AGG + chr5.4:64410227-64410246 MS.gene80639:CDS 50.0%
! GCATTTGGGGTAAGGTTACC+AGG + chr5.4:64410235-64410254 MS.gene80639:CDS 50.0%
! TATGTCAGGGGCACAGTTCT+TGG + chr5.4:64409449-64409468 MS.gene80639:CDS 50.0%
ACACCAAGGAGGAGGTTGCA+TGG + chr5.4:64410145-64410164 MS.gene80639:CDS 55.0%
ACCAGGCCTCATGGTAACAG+TGG + chr5.4:64410252-64410271 MS.gene80639:CDS 55.0%
GACGTCAAGGAGAACGCATC+AGG + chr5.4:64409324-64409343 MS.gene80639:CDS 55.0%
GAGGAGGTTGCATGGTATGC+TGG + chr5.4:64410153-64410172 MS.gene80639:CDS 55.0%
GGTAAGGTTACCAGGCCTCA+TGG + chr5.4:64410243-64410262 MS.gene80639:CDS 55.0%
TGAGGGGGTAAACACCAAGG+AGG + chr5.4:64410134-64410153 MS.gene80639:CDS 55.0%
GCCACTGTTACCATGAGGCC+TGG - chr5.4:64410256-64410275 None:intergenic 60.0%
GGGGGTAAACACCAAGGAGG+AGG + chr5.4:64410137-64410156 MS.gene80639:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 64409314 64410457 64409314 ID=MS.gene80639
chr5.4 mRNA 64409314 64410457 64409314 ID=MS.gene80639.t1;Parent=MS.gene80639
chr5.4 exon 64409314 64409345 64409314 ID=MS.gene80639.t1.exon1;Parent=MS.gene80639.t1
chr5.4 CDS 64409314 64409345 64409314 ID=cds.MS.gene80639.t1;Parent=MS.gene80639.t1
chr5.4 exon 64409445 64409480 64409445 ID=MS.gene80639.t1.exon2;Parent=MS.gene80639.t1
chr5.4 CDS 64409445 64409480 64409445 ID=cds.MS.gene80639.t1;Parent=MS.gene80639.t1
chr5.4 exon 64410092 64410320 64410092 ID=MS.gene80639.t1.exon3;Parent=MS.gene80639.t1
chr5.4 CDS 64410092 64410320 64410092 ID=cds.MS.gene80639.t1;Parent=MS.gene80639.t1
chr5.4 exon 64410416 64410457 64410416 ID=MS.gene80639.t1.exon4;Parent=MS.gene80639.t1
chr5.4 CDS 64410416 64410457 64410416 ID=cds.MS.gene80639.t1;Parent=MS.gene80639.t1
Gene Sequence

>MS.gene80639

ATGGTTAAAGGACGTCAAGGAGAACGCATCAGGTTTCTCTTCTTACCCTTCGATCTGTATCCTTTAACTCTTTTGATTTTATTGTTTCGATTTTCCTAATGTTGTTATTTTCATTTTGTGTTTTTAATCAGGCTTTATGTCAGGGGCACAGTTCTTGGATACAAGAGGTACTTGTTTTTCTTCGAAGATTTATTTTTCAGTTTTTGCTGTATTGGTTATATTAATTTAATGAAATCTAATTTCGTAAGCTAATTAAATCTAATTTGGGTTCGTAATATAGAAATATATAATATATGATTTTTTTAGCTGGGTTTTATTGGTGCTAAGAAATGTTTAATGTTGTTTTAGCTGGATATGTTGTTCTTTGAATTTTGTAGTTTATGTTAAGTTTTTAAAGTTTTCTGAAGTAAACCCAGCTTTTAATTTGTGTTTGTGATTGATAAATTTAAGAACCAAGACTCAATTTGGTCCTTCACAATATTTGCGGGCCCAATGTATCCTCGATAAAATATAATACCCAAACTAGTCCCAGCATTATCACAGTACAGGCAATCAATCCGCTTGTGATAATGAGTCTAGGACTAAATGATTACTGTAAGATTTGGGTATTATTTTTTGTATGGAACTAGATTAAGCAGTCGCAACATTACGAGAGACCAAATATATAATTTTTCTTCCGTCGTACATAATGTGTCTTCACCCTAGTAGTTCTTGATTTTGATGTTGATCTGGGTTGCTGGTGATTATTTGTGCTAAGAAATTGGTGATGTTGTTATAGGTCCAAGGTAAATCAATACCCAAACACCTCTCTTGTTCAGATTGAGGGGGTAAACACCAAGGAGGAGGTTGCATGGTATGCTGGGAAGAAATTGGCATACATTTACAAGGCCAAGGTGAAGAAGGATGGAAGCCACTATCGCTGCATTTGGGGTAAGGTTACCAGGCCTCATGGTAACAGTGGCATTGTCCGCGCAAAGTTCAAGTCTAACCTACCACCAAAATCAATGGTAATTCTTTAAGACATTTAAATGGTTTTTTTCTTTTCATTTTCACCAACTGTTTTATGGTTTCTGAAAGCTTTGGTGTTGATTTGTTTGTGCAGGGAGCCAGGGTTAGAGTATTTATGTATCCAAGCAATATATAA

Protein sequence

>MS.gene80639.t1

MVKGRQGERIRLYVRGTVLGYKRSKVNQYPNTSLVQIEGVNTKEEVAWYAGKKLAYIYKAKVKKDGSHYRCIWGKVTRPHGNSGIVRAKFKSNLPPKSMGARVRVFMYPSNI